Use target bed files as regions instead of bait intervals for SNV calling in WES samples #11
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| name: nf-core template version comment | |
| # This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. | |
| # It posts a comment to the PR, even if it comes from a fork. | |
| on: pull_request_target | |
| jobs: | |
| template_version: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Read template version from .nf-core.yml | |
| uses: nichmor/[email protected] | |
| id: read_yml | |
| with: | |
| config: ${{ github.workspace }}/.nf-core.yml | |
| - name: Install nf-core | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} | |
| - name: Check nf-core outdated | |
| id: nf_core_outdated | |
| run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} | |
| - name: Post nf-core template version comment | |
| uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 | |
| if: | | |
| contains(env.OUTPUT, 'nf-core') | |
| with: | |
| repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} | |
| allow-repeats: false | |
| message: | | |
| > [!WARNING] | |
| > Newer version of the nf-core template is available. | |
| > | |
| > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. | |
| > Please update your pipeline to the latest version. | |
| > | |
| > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). | |
| # |